Comparative RNA-Seq analysis reveals insights in Salmonella disease resistance of chicken; and database development as resource for gene expression in poultry

Authors: DAR, MASHOOQ - University Of Kashmir; AHMAD, SYED - University Of Kashmir; BHAT, BASHARAT - University Of Kashmir; DAR, TANVEER - University Of Kashmir; UL HAQ, ZULFQAR - University Of Kashmir; WANI, BASHARAT - University Of Kashmir; SHABIR, NADEEM - University Of Kashmir; KASHOO, ZAHID - University Of Kashmir; GANAI, NAZIR - University Of Kashmir; Heidari, Mohammad; SHAH, RIAZ - University Of Kashmir

Submitted to: Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/24/2022
Publication Date: 9/3/2022
Citation: Dar, M.A., Ahmad, S.M., Bhat, B.A., Dar, T.A., Ul Haq, Z., Wani, B.A., Shabir, N., Kashoo, Z.A., Ganai, N.A., Heidari, M., Shah, R.A. 2022. Comparative RNA-Seq analysis reveals insights in Salmonella disease resistance of chicken; and database development as resource for gene expression in poultry. Genomics. 114(5):110475. https://doi.org/10.1016/j.ygeno.2022.110475.
DOI: https://doi.org/10.1016/j.ygeno.2022.110475

Interpretive Summary: Salmonella causes considerable economic losses in countries that lack effective vaccination programs. Besides being resistant to diseases, indigenous chicken breeds are also a potential source of animal protein in developing countries. For understanding the disease resistance, an indigenous chicken line, Kashmir faverolla, and commercial broiler were selected. Gene expression analysis was performed after challenging the chickens with Salmonella Typhimurium. Comparative differential gene expression results showed that following infection, a total of 3153 genes and 1787 genes were differentially expressed in the liver and spleen, respectively. The differentially expressed genes included immune-related genes. Most of the genes involved in the innate and adaptive immune responses against bacterial infection were significantly enriched in the Kashmir faverolla line. On postmortem examination, the resistant birds showed small lesions in the liver compared to large necrotic lesions in susceptible birds. The pathological manifestations and gene expression profiling results suggest a balancing link between resistance and infection tolerance in Kashmir faverolla line. We also developed an online Poultry Infection Database (https://skuastk.org/pif/index.html), the first publicly available gene expression resource for disease resistance in chickens. The available database not only shows the data for gene expression in chicken tissues but also provides quick search, visualization and download capacity.

Technical Abstract: Salmonella, one of the major infectious diseases in poultry, causes considerable economic losses in terms of mortality and morbidity, especially in countries that lack effective vaccination programs. Besides being resistant to diseases, indigenous chicken breeds are also a potential source of animal protein in developing countries. For understanding the disease resistance, an indigenous chicken line Kashmir faverolla, and commercial broiler were selected. RNA-seq was performed after challenging the chicken with Salmonella Typhimurium. Comparative differential expression results showed that following infection, a total of 3153 genes and 1787 genes were differentially expressed in the liver and spleen, respectively. The genes that were differentially expressed included interleukins, cytokines, NOS2, Avß-defensins, toll-like receptors, and other immune-related gene families. Most of the genes and signaling pathways involved in the innate and adaptive immune responses against bacterial infection were significantly enriched in the Kashmir faverolla. Pathway analysis revealed that most of the enriched pathways were MAPK signaling pathway, NOD-like receptor signaling pathway, TLR signaling pathway, PPAR signaling pathway, endocytosis, etc. Surprisingly some immune-related genes like TLRs were upregulated in the susceptible chicken breed. On postmortem examination, the resistant birds showed small lesions in the liver compared to large necrotic lesions in susceptible birds. The pathological manifestations and RNA sequencing results suggest a balancing link between resistance and infection tolerance in Kashmir faverolla. Here we also developed an online Poultry Infection Database (https://skuastk.org/pif/index.html), the first publicly available gene expression resource for disease resistance in chickens. The available database not only shows the data for gene expression in chicken tissues but also provides quick search, visualization and download capacity.